What's all this about the height? Meaningless. By far the most important thing to consider is whether he can embody the role. Wolverine is described as 5'3" in the comics. Hugh Jackman is a full foot taller than that, and he's great for the role. He carries Wolverine. That's what matters. Also, they can shoot Cruise to make him come off a bit taller, just like they shot Jackman to seem shorter in the first couple films (they've pretty much scrapped that now).
That said, I don't think it's a good idea. He has too much baggage. People aren't going to see Batman. They're going to see Tom Cruise. He's a great actor, but he's really shot himself him in the foot with all his tabloid attention. That does matter. Even without all that, I don't think he would be a good choice. He has this boyish intensity. It works well for most of his roles, but he doesn't really do sullen and brooding. Not that he couldn't. He definitely has range, but I think it would be best to go for someone who has that a little more in their repertoire.
Someone mentioned Jon Hamm. I think that's a little closer.